Genomic Surveillance for SARS-CoV-2 During the COVID-19 Pandemic: Collaborative Experience at Southeast Michigan

Regional genomic surveillance is essential for tracking viral evolution and informing targeted public health responses. During the COVID-19 pandemic, we established a collaborative genomic surveillance pipeline for SARS-CoV-2 in Southeast Michigan to support national surveillance efforts and guide local pandemic response strategies. A partnership between Wayne State University (WSU), Detroit Health Department (DHD), Henry Ford Health (HFH), Wayne Health Mobile Unit (WHMU), and Michigan Department of Health and Human Services (MDHHS) was established to collect, sequence, and analyze SARS-CoV-2 samples. Samples underwent automated nucleic acid extraction, PCR testing, and whole genome sequencing at WSU's Integrative Biosciences Center (IBio). Consensus genome sequences were analyzed using high-performance computing infrastructure for lineage assignment and variant identification. Between January 2022 and July 2024, we collected and archived 7,508 samples, with 6,235 (83.0%) successfully sequenced. Analysis of 4,637 Henry Ford Health samples revealed geographic distribution across 295 Michigan ZIP codes, representing 5.7 million residents. Cases were predominantly female (57%) and aged 20-49 years (33%). Omicron was the most prevalent variant (64% of cases). Variant distributions showed strong correlation (r = 0.98) with Michigan trends reported in GISAID, validating the pipeline's accuracy. Black individuals showed 1.4-fold higher infection rates compared to White individuals, though social deprivation index appeared to be a stronger predictor of mortality than race. We successfully established a regional genomic surveillance pipeline that accurately tracked SARS-CoV-2 variant circulation in Southeast Michigan. This framework demonstrates the value of academic-public health partnerships and provides a replicable model for pathogen surveillance systems adaptable to future infectious disease outbreaks.